For many years Cowles Mountain was locally known as "S" Mountain. In 1931, 500 students from San Diego State College, now San Diego State University (SDSU), painted a 400-foot-tall (120 m) letter "S" on the side of the mountain, after which it took on its popular name.[3] In April 1942, during World War II, the local military ordered the S covered up for the sake of national security. After the war the painting tradition was resurrected.

In the 1970s, the annual repainting tradition was ceased for environmental and habitat protection, but suffered a brief resurgence in the late 1980s. The "S" has not been repainted for nearly three decades.

The main trail to the summit is a popular hiking destination taking hundreds of people per day to a 360-degree panorama of San Diego County. The hike to the top is 1.5 miles (2.4 km) long and an elevation change of about 950 feet (290 m). This trail is on the corner of Golfcrest Drive and Navajo Road. A much-less-used but maintained trail begins near the intersection of Boulder Lake Avenue and Barker way. This trail meets the main trail near the summit.

On March 25, 2013 the trails of Cowles were closed for maintenance.[4] The trails were reopened in May 2013 after several improvements to water drainage and rock steps.[5]

Cowles Mountain consists of Jurassic and early Cretaceous metavolcanic and shallow intrusive igneous rocks that are resistant to erosion, and never covered by later Cretaceous and Tertiary sedimentary overburden. Small plateaus on the south and east slopes are the remnants of an extensive terrestrial, near sea level erosional surface called the Poway Terrace that are now about 1,200 feet (370 m) in elevation.

A prominent former seacliff on the west side rises above a now-dry wave-cut terrace, now mostly covered with suburban developments, at about 600 feet (180 m) in elevation.